Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009277.1 Corchorus capsularis cultivar CVL-1 contig09298, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25843
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1940 original size:26 final size:26
Alignment explanation
Indices: 1899--1963 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
1889 TGGACCTAAA
* *
1899 GACAAAAATGCTCTTGA-AGTGAAAAT
1 GACAAAAATGCCCTTGAGA-CGAAAAT
* *
1925 GACCAAAATGCCCTTGGGACGAAAAT
1 GACAAAAATGCCCTTGAGACGAAAAT
1951 GACAAAAATGCCC
1 GACAAAAATGCCC
1964 CTGGCAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (26 bp):
GACAAAAATGCCCTTGAGACGAAAAT
Found at i:8349 original size:17 final size:17
Alignment explanation
Indices: 8327--8360 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8317 TACATCTTAT
8327 AATTTTCTAATTTTTCC
1 AATTTTCTAATTTTTCC
* *
8344 AATTTTTTCATTTTTCC
1 AATTTTCTAATTTTTCC
8361 TTCTCTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTCTAATTTTTCC
Found at i:8396 original size:19 final size:19
Alignment explanation
Indices: 8346--8397 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
8336 ATTTTTCCAA
8346 TTTTTTCA-TTTTTCCTTC
1 TTTTTTCATTTTTTCCTTC
* *
8364 TCTTTTCATTTTTTTCTTC
1 TTTTTTCATTTTTTCCTTC
8383 TTTTTTCATTTTTTC
1 TTTTTTCATTTTTTC
8398 AAATTTTGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTCATTTTTTCCTTC
Found at i:8404 original size:18 final size:18
Alignment explanation
Indices: 8337--8404 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
8327 AATTTTCTAA
*
8337 TTTTTCCAATTTTTTCAT
1 TTTTTCTAATTTTTTCAT
* ** *
8355 TTTTCCTTCTCTTTTCATT
1 TTTTTCTAATTTTTTCA-T
**
8374 TTTTTCTTCTTTTTTCAT
1 TTTTTCTAATTTTTTCAT
*
8392 TTTTTCAAATTTT
1 TTTTTCTAATTTT
8405 GACCTAAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 23 0.59
19 16 0.41
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCTAATTTTTTCAT
Found at i:12410 original size:26 final size:25
Alignment explanation
Indices: 12346--12419 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 25
12336 AGCGGACTTG
12346 AAATAGACCAAAATGCCCCTGAATGTGC
1 AAAT-GACCAAAATGCCCCT--ATGTGC
*
12374 AAATGAGCAAAATGCCCCTA-GTGC
1 AAATGACCAAAATGCCCCTATGTGC
12398 AAAAATGACCAAAATGCCCCTA
1 --AAATGACCAAAATGCCCCTA
12420 AGTGACCCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.10
25 1 0.02
26 19 0.45
27 14 0.33
28 4 0.10
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (25 bp):
AAATGACCAAAATGCCCCTATGTGC
Found at i:15039 original size:9 final size:9
Alignment explanation
Indices: 15025--15054 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
15015 AAACTAGTGC
15025 AGAAAACTA
1 AGAAAACTA
15034 AGAAAACTA
1 AGAAAACTA
*
15043 AGAAAATTA
1 AGAAAACTA
15052 AGA
1 AGA
15055 CTCAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (9 bp):
AGAAAACTA
Found at i:22132 original size:18 final size:19
Alignment explanation
Indices: 22109--22149 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
22099 CGGAAAGAGA
22109 CCTCCCTCCTCT-TCCATT
1 CCTCCCTCCTCTCTCCATT
* *
22127 CCTCCCTTCTCTCTCGATT
1 CCTCCCTCCTCTCTCCATT
22146 CCTC
1 CCTC
22150 TCTCTCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.05, C:0.54, G:0.02, T:0.39
Consensus pattern (19 bp):
CCTCCCTCCTCTCTCCATT
Found at i:23934 original size:18 final size:18
Alignment explanation
Indices: 23911--23948 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
23901 TTAACGATGA
23911 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
23929 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
23947 AC
1 AC
23949 CACAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:24685 original size:122 final size:124
Alignment explanation
Indices: 24537--24839 Score: 344
Period size: 128 Copynumber: 2.4 Consensus size: 124
24527 CTAACAAGAC
* * * *
24537 TTTGGAATCGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGGTTTGA-AACCAACACG-A-
1 TTTGGAATCGGAACAAGAAACCCTCGATTAGAGACCTCAAGCAGGATTTGAGAACCAA-ACGAAT
*
24599 TT-TTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAACAATGAAACGAAA
65 TTATTGAAACAAGAAACCCTCGACTAGAGACCTCAAGCAGGATTTG-ACAATGAAACGAAA
* * ** **
24659 TTTGGAATTGGAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGAATGAAACGACAT
1 TTTGGAATCGGAACAAGAAACCCTCGATTAGAGACCTCAAGCAGGATTTGAGAACCAAACGA-AT
* * * ** *
24724 TTGGAATTGGAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGCAATGAAACGAAA
65 TT---ATTGAAACAAGAAACCCTCGACTAGAGACCTCAAGCAGGATTTGACAATGAAACGAAA
* **
24787 TTTGGAATCGGAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGA
1 TTTGGAATCGGAACAAGAAACCCTCGATTAGAGACCTCAAGCAGGATTTGAGA
24840 TAAATAAGAA
Statistics
Matches: 155, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
122 46 0.30
123 4 0.03
124 1 0.01
125 2 0.01
128 65 0.42
129 37 0.24
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (124 bp):
TTTGGAATCGGAACAAGAAACCCTCGATTAGAGACCTCAAGCAGGATTTGAGAACCAAACGAATT
TATTGAAACAAGAAACCCTCGACTAGAGACCTCAAGCAGGATTTGACAATGAAACGAAA
Found at i:24744 original size:64 final size:64
Alignment explanation
Indices: 24605--24839 Score: 373
Period size: 64 Copynumber: 3.7 Consensus size: 64
24595 ACGATTTTGA
* * * ** *
24605 AACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAACAATGAAACGAAATTTGGAATTGG
1 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTG-AGAATGAAACGAAATTTGGAATTGG
*
24670 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGAATGAAACGACATTTGGAATTGG
1 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGAATGAAACGAAATTTGGAATTGG
*
24734 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTG-GCAATGAAACGAAATTTGGAATCGG
1 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAG-AATGAAACGAAATTTGGAATTGG
24798 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGA
1 AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGA
24840 TAAATAAGAA
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.01
64 123 0.77
65 35 0.22
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (64 bp):
AACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGAGAATGAAACGAAATTTGGAATTGG
Found at i:25762 original size:1 final size:1
Alignment explanation
Indices: 25758--25791 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
25748 TTTTTTTAGC
25758 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25792 CCAGCTTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25766 original size:46 final size:46
Alignment explanation
Indices: 25668--25766 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
25658 TACTTATTTA
* *
25668 TCTTTTTCCGACCTCTTTCTATTTTAGGCCAAGTTTTTTTTTACTT
1 TCTTTTTCCGACCTCTTTCTATTTTAGGCCAACTCTTTTTTTACTT
* *
25714 TCTTTTTCTGACCTCTTTCTATTTTAGGCC-CCTCTTTTTTTAGCTT
1 TCTTTTTCCGACCTCTTTCTATTTTAGGCCAACTCTTTTTTTA-CTT
*
25760 TTTTTTT
1 TCTTTTT
25767 TTTTTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 9 0.19
46 38 0.81
ACGTcount: A:0.10, C:0.22, G:0.08, T:0.60
Consensus pattern (46 bp):
TCTTTTTCCGACCTCTTTCTATTTTAGGCCAACTCTTTTTTTACTT
Done.